A Thiamine-Dependent Enzyme Utilizes an Active Tetrahedral Intermediate in Vitamin K Biosynthesis

Enamine
is a well-known reactive intermediate mediating essential
thiamine-dependent catalysis in central metabolic pathways. However,
this intermediate is not found in the thiamine-dependent catalysis
of the vitamin K biosynthetic enzyme MenD. Instead, an active tetrahedral
post-decarboxylation intermediate is stably formed in the enzyme and
was structurally determined at 1.34 Å resolution in crystal.
This intermediate takes a unique conformation that allows only one
proton between its tetrahedral reaction center and the exo-ring nitrogen
atom of the aminopyrimidine moiety in the cofactor with a short distance
of 3.0 Å. It is readily convertible to the final product of the
enzymic reaction with a solvent-exchangeable proton at its reaction
center. These results show that the thiamine-dependent enzyme utilizes
a tetrahedral intermediate in a mechanism distinct from the enamine
catalytic chemistry.